For the LIMMA package you should be able to read in the fore- and background data directly from the ArrayWoRx output .res-files using these lines, when you have the output files grouped together in your work directory: files<-dir(pattern="*\\.res") RG<-read.maimages(files, columns=list(Rf="S1", Gf="S2", Rb="B1", Gb="B2")) You need to check the settings in the scanner software regarding which dye goes into which channel. Per Gregersen